Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.17.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.78791	0.244
27DAP/17DAP	1.15217	0.99
39DAP/27DAP	1.12361	0.876
41DAP/39DAP	1.06588	0.962
42DAP/41DAP	1.3671	0.626
43DAP/42DAP	1.15776	0.809
47DAP/43DAP	0.56878	0.076
52DAP/47DAP	1.76802	0.256
57DAP/52DAP	0.7508	0.635

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91104	0.231
17DAP/reference	0.75031	0.007
27DAP/reference	0.92505	0.385
39DAP/reference	0.74672	0.027
41DAP/reference	0.65559	0.016
42DAP/reference	0.90389	0.115
43DAP/reference	0.87154	0.088
47DAP/reference	0.90722	0.148
52DAP/reference	1.11937	0.217
57DAP/reference	1.24621	0.01

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80606	0.211
27DAP/17DAP	1.27539	0.511
39DAP/27DAP	0.7065	0.035
41DAP/39DAP	1.32267	0.087
42DAP/41DAP	1.13354	0.773
43DAP/42DAP	1.46131	0.021
47DAP/43DAP	1.03225	0.926
52DAP/47DAP	1.56357	0.301
57DAP/52DAP	4.51875	0.029
57DAP/7DAP	1.65538	0.22

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03291	1
17DAP/reference	1.0656	0.822
27DAP/reference	0.99207	0.571
39DAP/reference	1.14916	0.252
41DAP/reference	1.32119	0.199
42DAP/reference	1.26081	0.076
43DAP/reference	1.77969	0.007
47DAP/reference	1.09272	0.7
52DAP/reference	1.19356	0.055
57DAP/reference	1.01779	0.648

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86222	0.231
17DAP/reference	0.66661	0.008
27DAP/reference	0.79925	0.108
39DAP/reference	0.89497	0.093
41DAP/reference	0.98295	0.481
42DAP/reference	0.92492	0.169
43DAP/reference	0.74574	0.062
47DAP/reference	0.78713	0.021
52DAP/reference	0.81802	0.006
57DAP/reference	0.63745	0.003

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40089	0.086
17DAP/reference	0.90257	0.364
27DAP/reference	1.16237	0.07
39DAP/reference	0.96256	0.464
41DAP/reference	0.96186	0.56
42DAP/reference	1.12358	0.272
43DAP/reference	0.97004	0.484
47DAP/reference	0.84642	0.063
52DAP/reference	1.3474	0.312
57DAP/reference	1.14363	0.138

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.34784	0.966
26DAP/20DAP	1.23318	0.558
34DAP/26DAP	0.88228	0.61
51DAP/34DAP	0.74384
52DAP/51DAP	0.95533	1
53DAP/52DAP	1.20225	0.398
55DAP/53DAP	0.69403	0.067
57DAP/55DAP	0.9481	0.619
62DAP/57DAP	1.2034	0.257
68DAP/62DAP	2.27026	0.105
68DAP/14DAP	2.31257	0.023

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.03543	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.17232	0.017
Immature Eggplant/Mature Eggplant	0.53681	0.074
Ripe Pepper/Ripe Tomato	0.13581	0.224
Mature Eggplant/Ripe Tomato	0.59743	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.20727
1-1-2/M82	1.17766
12-2/M82	1.08334
12-4/M82	1.05375	1
1-3/M82	N/A	N/A
2-1-1/M82	1.09941
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.27005
4-3/M82	N/A	N/A
5-3/M82	0.6645	0.419
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.81406	0.385
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.91956
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.00387	1
IL12-4/WTpooled	1.09853	0.839
IL1-4/WTpooled	1.00135	1
WT/WTpooled	1.09443	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.29444	0.309

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.18502	0.774
DC3000/delta hrp 6h	0.91014	0.95
DC3000/delta hrp 12h	0.97086	1
DC3000/delta hrp 24h	1.26099	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17999	0.384
DC3000 delta B/DC3000 delta AB	1.29202	0.115

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.79698	1
Exp 36h	1.17855	1
Exp 60h	0.97335	0.994

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.98479	1
Var 0h	1.00524	1
Var 12h I row2-row1	1.02119	1
Var 12h NI row2-row1	1.20759	0.235
Var 36h I row2-row1	0.98161	1
Var 36h NI row2-row1	0.97123	0.791
Var 60h I row2-row1	0.92321	0.439
Var 60h NI row2-row1	1.06337	1
Time course 0hI-0hNI	0.88348	0.222
Time course 12hI-12hNI	0.92868	0.535
Time course 36hI-36hNI	0.80024	0.047
Time course 60hI-60hNI	1.94851	0.008

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.30092	0.397
transgenic ySAMdc/azygous control (breaker)	0.33383	0.142
transgenic ySAMdc/azygous control (red)	1.27746	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.58619	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.68067	0.172
Manapal/WT (break)	1.25188	1
Manapal/WT (red)	1.14079	1